Difference between revisions of "Task3 Hemochromatosis Protocol"
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Bernhoferm (talk | contribs) (→Disorder) |
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=== Disorder === |
=== Disorder === |
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| + | |||
| + | IUPred predictions: |
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| + | <source lang="bash"> |
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| + | #!/bin/bash |
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| + | |||
| + | #Disorder |
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| + | DIS="/mnt/home/student/bernhoferm/mstrprkt/task3/disorder" |
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| + | cd /opt/iupred/ |
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| + | |||
| + | iupred $DIS/fasta/Q30201.fasta long > $DIS/pred/Q30201.pred |
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| + | iupred $DIS/fasta/P10775.fasta long > $DIS/pred/P10775.pred |
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| + | iupred $DIS/fasta/Q9X0E6.fasta long > $DIS/pred/Q9X0E6.pred |
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| + | iupred $DIS/fasta/Q08209.fasta long > $DIS/pred/Q08209.pred |
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| + | </source> |
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=== Transmembrane Helices === |
=== Transmembrane Helices === |
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Revision as of 12:00, 17 May 2012
Contents
Data Acquisition
Retrieve all sequences: <source lang="bash">
- !/bin/bash
- Secondary Structure
cd /mnt/home/student/bernhoferm/mstrprkt/task3/ss/fasta/
wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P10775.fasta wget http://www.uniprot.org/uniprot/Q9X0E6.fasta wget http://www.uniprot.org/uniprot/Q08209.fasta
- Disorder
cd /mnt/home/student/bernhoferm/mstrprkt/task3/disorder/fasta/
wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P10775.fasta wget http://www.uniprot.org/uniprot/Q9X0E6.fasta wget http://www.uniprot.org/uniprot/Q08209.fasta
- Transmembrane Helices
cd /mnt/home/student/bernhoferm/mstrprkt/task3/tmh/fasta/
wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P35462.fasta wget http://www.uniprot.org/uniprot/Q9YDF8.fasta wget http://www.uniprot.org/uniprot/P47863.fasta
- Signal Peptides
cd /mnt/home/student/bernhoferm/mstrprkt/task3/sp/fasta/
wget http://www.uniprot.org/uniprot/Q30201.fasta wget http://www.uniprot.org/uniprot/P02768.fasta wget http://www.uniprot.org/uniprot/P47863.fasta wget http://www.uniprot.org/uniprot/P11279.fasta </source>
Secondary Structure
ReProf predictions: <source lang="bash">
- !/bin/bash
- Secondary Structure
cd /mnt/home/student/bernhoferm/mstrprkt/task3/ss/fasta/
reprof -i Q30201.fasta -o ../pred/ &> ../Q30201.log reprof -i P10775.fasta -o ../pred/ &> ../P10775.log reprof -i Q9X0E6.fasta -o ../pred/ &> ../Q9X0E6.log reprof -i Q08209.fasta -o ../pred/ &> ../Q08209.log </source>
Disorder
IUPred predictions: <source lang="bash">
- !/bin/bash
- Disorder
DIS="/mnt/home/student/bernhoferm/mstrprkt/task3/disorder" cd /opt/iupred/
iupred $DIS/fasta/Q30201.fasta long > $DIS/pred/Q30201.pred iupred $DIS/fasta/P10775.fasta long > $DIS/pred/P10775.pred iupred $DIS/fasta/Q9X0E6.fasta long > $DIS/pred/Q9X0E6.pred iupred $DIS/fasta/Q08209.fasta long > $DIS/pred/Q08209.pred </source>
